Rapid displacement of SARS-CoV-2 variant Delta by Omicron revealed by allele-specific PCR in wastewater

•Allele-specific RT-qPCR assay for quantitative detection of the Omicron variant.•Assay validated against 10-month longitudinal wastewater treatment plant samples.•SARS-CoV-2 RNA concentrations and variant frequencies in wastewater agree with clinical data.•Assays reveal the rapid displacement of th...

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Published in:Water research (Oxford) 2022-08, Vol.221, p.118809-118809, Article 118809
Main Authors: Lee, Wei Lin, Armas, Federica, Guarneri, Flavia, Gu, Xiaoqiong, Formenti, Nicoletta, Wu, Fuqing, Chandra, Franciscus, Parisio, Giovanni, Chen, Hongjie, Xiao, Amy, Romeo, Claudia, Scali, Federico, Tonni, Matteo, Leifels, Mats, Chua, Feng Jun Desmond, Kwok, Germaine WC, Tay, Joey YR, Pasquali, Paolo, Thompson, Janelle, Alborali, Giovanni Loris, Alm, Eric J
Format: Article
Language:English
Subjects:
Alleles
COVID-19
COVID-19 Testing
Humans
Omicron
Real-Time Polymerase Chain Reaction
RNA, Viral
RT-qPCR
SARS-CoV-2
SARS-CoV-2 - genetics
Surveillance
Vaccine breakthrough
Variant
Wastewater
Wastewater - analysis
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Summary:•Allele-specific RT-qPCR assay for quantitative detection of the Omicron variant.•Assay validated against 10-month longitudinal wastewater treatment plant samples.•SARS-CoV-2 RNA concentrations and variant frequencies in wastewater agree with clinical data.•Assays reveal the rapid displacement of the Delta variant by the Omicron variant.•Assays derived enable accurate tracking of the dynamics of variant displacement. On November 26, 2021, the B.1.1.529 COVID-19 variant was classified as the Omicron variant of concern (VOC). Reports of higher transmissibility and potential immune evasion triggered flight bans and heightened health control measures across the world to stem its distribution. Wastewater-based surveillance has demonstrated to be a useful complement for clinical community-based tracking of SARS-CoV-2 variants. Using design principles of our previous assays that detect SARS-CoV-2 variants (Alpha and Delta), we developed an allele-specific RT-qPCR assay which simultaneously targets the stretch of mutations from Q493R to Q498R for quantitative detection of the Omicron variant in wastewater. We report their validation against 10-month longitudinal samples from the influent of a wastewater treatment plant in Italy. SARS-CoV-2 RNA concentrations and variant frequencies in wastewater determined using these variant assays agree with clinical cases, revealing rapid displacement of the Delta variant by the Omicron variant within three weeks. These variant trends, when mapped against vaccination rates, support clinical studies that found the rapid emergence of SARS-CoV-2 Omicron variant being associated with an infection advantage over Delta in vaccinated persons. These data reinforce the versatility, utility and accuracy of these open-sourced methods using allele-specific RT-qPCR for tracking the dynamics of variant displacement in communities through wastewater for informed public health responses. [Display omitted]
ISSN:0043-1354
1879-2448
DOI:10.1016/j.watres.2022.118809